RetrogeneDB ID: retro_cjac_4159

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:45668093..45668745(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CHMP5
• Ensembl ID: ENSCJAG00000008104
• Aliases: None
• Description: charged multivesicular body protein 5 [Source:HGNC Symbol;Acc:26942]

Sequence

>retro_cjac_4159
ATGAACCAATTCTTCGGGAAAGTAAAACCCAAGGCTCCGCCACCCAGCCTGACTGACCACATTGGCACTGTGAACAGCAG
GGCAGAGTCCATTGACAAGAAGATTTCTCGATTGGATGCTGAGCTAGTGAAGTATAAGGATCAGATCAAGAAGATGAGAG
AGGGTCCTGCAAAGAATACGGTCAAGCAGAAAGCCTTGCGAGTTTCAAAGTAAAAGTGGTTGTATGAGCAGCAGCAGGAC
AATCTTGCCCAGCAGTTGTTCAACATGGAACAAGCCAATTATACCATTCAGTAATTGAAGGACACTAAGACCATGGGTGA
TGCTATGAAATTGGGAGTACAAGGAAATGAAGAAGGCATACAAGTGAAAATTGACCAGATGAGGATTTACAAGACCAGCT
AGAGGATATGATGGAAGTTGCAAATGAAATCCAAGAATCACTGAGTCGCAATTATGGCAACCCAGAACTGGATGAAGATG
ACCTGGAAGCAGAGTTGGATGGACTGAATGATGAGCTTCTGGCTGATGAAGACAGTTCTTATTTGGATGAGGCAGCATGT
GCACCTACAATGCCAGAATGTGTTTCTACCGACACAAAAACGAGGATGGAGCTCCGGTGGATGAATTTGGATTGCCACAG
ATCCCTGCTTCA

Alignment

ORF - retro_cjac_4159 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNRFFGKAKPKAPPPSLTDCIGTVDSRAESIDKKISRLDAELVKYKDQIKKMREGPAKNMVKQKALRVLK
          MN.FFGK.KPKAPPPSLTD.IGTV.SRAESIDKKISRLDAELVKYKDQIKKMREGPAKN.VKQKALRV.K
Retrocopy MNQFFGKVKPKAPPPSLTDHIGTVNSRAESIDKKISRLDAELVKYKDQIKKMREGPAKNTVKQKALRVSK

Parental  QKRMYEQQRDNLAQQSFNMEQANYTIQSLKDTKTTVDAMKLGVKEMKKAYKQVKIDQI-EDLQDQLEDMM
          .K..YEQQ.DNLAQQ.FNMEQANYTIQ.LKDTKT..DAMKLGV........QVKIDQ..EDLQDQLEDMM
Retrocopy *KWLYEQQQDNLAQQLFNMEQANYTIQ*LKDTKTMGDAMKLGVQGNEEGI-QVKIDQM<EDLQDQLEDMM

Parental  EDANEIQEALSRSYGTPELDEDDLEAELDALGDELLADEDSSYLDEAASAPAIPEGVPTDT-KNKDGVLV
          E.ANEIQE.LSR.YG.PELDEDDLEAELD.L.DELLADEDSSYLDEAA.AP..PE.V.TDT.KN.DG..V
Retrocopy EVANEIQESLSRNYGNPELDEDDLEAELDGLNDELLADEDSSYLDEAACAPTMPECVSTDT<KNEDGAPV

Parental  DEFGLPQIPAS
          DEFGLPQIPAS
Retrocopy DEFGLPQIPAS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.16 RPM	22.72 RPM
SRP051959_heart	0.04 RPM	20.33 RPM
SRP051959_kidney	0.00 RPM	33.10 RPM
SRP051959_liver	0.09 RPM	20.99 RPM
SRP051959_lung	0.42 RPM	25.08 RPM
SRP051959_lymph_node	0.62 RPM	13.70 RPM
SRP051959_skeletal_muscle	0.04 RPM	16.68 RPM
SRP051959_spleen	0.21 RPM	25.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4159 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4159 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4159 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012672	1 retrocopy	retro_chof_2045,
Callithrix jacchus	ENSCJAG00000008104	2 retrocopies	retro_cjac_2868, retro_cjac_4159 ,
Cavia porcellus	ENSCPOG00000003467	2 retrocopies	retro_cpor_1221, retro_cpor_1306,
Dipodomys ordii	ENSDORG00000006280	2 retrocopies	retro_dord_292, retro_dord_764,
Echinops telfairi	ENSETEG00000001424	1 retrocopy	retro_etel_2126,
Homo sapiens	ENSG00000086065	2 retrocopies	retro_hsap_4822, retro_hsap_494,
Microcebus murinus	ENSMICG00000012113	2 retrocopies	retro_mmur_369, retro_mmur_843,
Myotis lucifugus	ENSMLUG00000011045	1 retrocopy	retro_mluc_954,
Macaca mulatta	ENSMMUG00000020149	1 retrocopy	retro_mmul_2573,
Monodelphis domestica	ENSMODG00000004012	2 retrocopies	retro_mdom_2002, retro_mdom_595,
Mus musculus	ENSMUSG00000028419	1 retrocopy	retro_mmus_1469,
Nomascus leucogenys	ENSNLEG00000005158	2 retrocopies	retro_nleu_2197, retro_nleu_2420,
Otolemur garnettii	ENSOGAG00000000774	6 retrocopies	retro_ogar_2072, retro_ogar_2190, retro_ogar_2386, retro_ogar_2504, retro_ogar_2509, retro_ogar_916,
Pongo abelii	ENSPPYG00000019137	2 retrocopies	retro_pabe_239, retro_pabe_3750,
Pan troglodytes	ENSPTRG00000020857	2 retrocopies	retro_ptro_3210, retro_ptro_373,
Rattus norvegicus	ENSRNOG00000008672	1 retrocopy	retro_rnor_2614,
Ictidomys tridecemlineatus	ENSSTOG00000026573	1 retrocopy	retro_itri_424,
Tupaia belangeri	ENSTBEG00000003486	5 retrocopies	retro_tbel_1626, retro_tbel_1894, retro_tbel_2407, retro_tbel_3364, retro_tbel_3494,
Tursiops truncatus	ENSTTRG00000010575	1 retrocopy	retro_ttru_338,